Are you trying to debug the 29466 using the ICE cube connected to the 29466 through the 5 pin ISSP connector?

The 5 pin connector is only for programming the device. It is not possible to debug the device using the ISSP connector. For debugging the device you need to use a pod, which you would have got along with the ICE CUBE. The pod connects to the 2x10 pin header on the ICE CUBE that is marked as POD. The pod will have to be placed in the place of the actual device on the target board using a pod foot. For example, if you are trying to debug a 28 pin SSOP device, you need to get the pod feet from the below link.

This pod feed has to be soldered on the target board in place of the 29466. The pod will fix on the top of ths pod feet and will be connected to the ICE CUBE. Now the pod will emulate the 29466 and through the ICE CUBE has a connectivity to the PC for debugging. Another way to debug is to use a OCD version of the chip and create a special version of your target board. Check out below application note.